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Author R Scott McIsaac

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A tps1Δ persister-like state in Saccharomyces cerevisiae is regulated by MKT1.

Patrick A Gibney, Anqi Chen, Ariel Schieler, Jonathan C Chen, Yifan Xu, David G Hendrickson, R Scott McIsaac, Joshua D Rabinowitz, David Botstein,

Trehalose metabolism in yeast has been linked to a variety of phenotypes, including heat resistance, desiccation tolerance, carbon-source utilization, and sporulation. The relationships among the several phenotypes of mutants unable to synthesize trehalose are not understood, even though the pathway is highly conserved. One of these phenotypes is that tps1Δ ... Read more >>

PLoS ONE (PloS one)
[2020, 15(5):e0233779]

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Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses.

Yiming Kang, Nikhil R Patel, Christian Shively, Pamela Samantha Recio, Xuhua Chen, Bernd J Wranik, Griffin Kim, R Scott McIsaac, Robi Mitra, Michael R Brent,

A high-confidence map of the direct, functional targets of each transcription factor (TF) requires convergent evidence from independent sources. Two significant sources of evidence are TF binding locations and the transcriptional responses to direct TF perturbations. Systematic data sets of both types exist for yeast and human, but they rarely ... Read more >>

Genome Res. (Genome research)
[2020, 30(3):459-471]

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Monomerization of far-red fluorescent proteins.

Timothy M Wannier, Sarah K Gillespie, Nicholas Hutchins, R Scott McIsaac, Sheng-Yi Wu, Yi Shen, Robert E Campbell, Kevin S Brown, Stephen L Mayo,

Anthozoa-class red fluorescent proteins (RFPs) are frequently used as biological markers, with far-red (λem ∼ 600-700 nm) emitting variants sought for whole-animal imaging because biological tissues are more permeable to light in this range. A barrier to the use of naturally occurring RFP variants as molecular markers is that all ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2018, 115(48):E11294-E11301]

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Simultaneous Profiling of DNA Accessibility and Gene Expression Dynamics with ATAC-Seq and RNA-Seq.

David G Hendrickson, Ilya Soifer, Bernd J Wranik, David Botstein, R Scott McIsaac,

This chapter describes sequencing-based methods for profiling dynamic changes in DNA accessibility and gene expression in Saccharomyces cerevisiae. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) is a powerful technique for identifying nucleosome-free regions of the genome. Combining ATAC-Seq with RNA Sequencing (RNA-Seq) is a rapid approach for studying the ... Read more >>

Methods Mol. Biol. (Methods in molecular biology (Clifton, N.J.))
[2018, 1819:317-333]

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An estradiol-inducible promoter enables fast, graduated control of gene expression in fission yeast.

Makoto J Ohira, David G Hendrickson, R Scott McIsaac, Nicholas Rhind,

The fission yeast Schizosaccharomyces pombe lacks a diverse toolkit of inducible promoters for experimental manipulation. Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium. In particular, no S. pombe inducible promoter systems exhibit a linear dose-response, which would allow ... Read more >>

Yeast (Yeast (Chichester, England))
[2017, 34(8):323-334]

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An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast

Makoto Ohira, David Hendrickson, Scott McIsaac, Nicholas Rhind,

ABSTRACT The fission yeast Schizosaccharomyces pombe lacks a diverse toolkit of inducible promoters for experimental manipulation. Available inducible promoters suffer from slow induction kinetics, limited control of expression levels and/or a requirement for defined growth medium. In particular, no S. pombe inducible promoter systems exhibit a linear dose response, which ... Read more >>

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Unraveling the message: insights into comparative genomics of the naked mole-rat.

Kaitlyn N Lewis, Ilya Soifer, Eugene Melamud, Margaret Roy, R Scott McIsaac, Matthew Hibbs, Rochelle Buffenstein,

Animals have evolved to survive, and even thrive, in different environments. Genetic adaptations may have indirectly created phenotypes that also resulted in a longer lifespan. One example of this phenomenon is the preternaturally long-lived naked mole-rat. This strictly subterranean rodent tolerates hypoxia, hypercapnia, and soil-based toxins. Naked mole-rats also exhibit ... Read more >>

Mamm. Genome (Mammalian genome : official journal of the International Mammalian Genome Society)
[2016, 27(7-8):259-278]

Cited: 13 times

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From yeast to human: exploring the comparative biology of methionine restriction in extending eukaryotic life span.

R Scott McIsaac, Kaitlyn N Lewis, Patrick A Gibney, Rochelle Buffenstein,

Methionine restriction is a widely reported intervention for increasing life span in several model organisms. Low circulating levels of methionine are evident in the long-lived naked mole-rat, suggesting that it naturally presents with a life-extending phenotype akin to that observed in methionine-restricted animals. Similarly, long-lived dwarf mice also appear to ... Read more >>

Ann. N. Y. Acad. Sci. (Annals of the New York Academy of Sciences)
[2016, 1363:155-170]

Cited: 17 times

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Recent advances in engineering microbial rhodopsins for optogenetics.

R Scott McIsaac, Claire N Bedbrook, Frances H Arnold,

Protein engineering of microbial rhodopsins has been successful in generating variants with improved properties for applications in optogenetics. Members of this membrane protein family can act as both actuators and sensors of neuronal activity. Chimeragenesis, structure-guided mutagenesis, and directed evolution have proven effective strategies for tuning absorption wavelength, altering ion ... Read more >>

Curr. Opin. Struct. Biol. (Current opinion in structural biology)
[2015, 33:8-15]

Cited: 13 times

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Directed evolution of a far-red fluorescent rhodopsin.

R Scott McIsaac, Martin K M Engqvist, Timothy Wannier, Adam Z Rosenthal, Lukas Herwig, Nicholas C Flytzanis, Eleonora S Imasheva, Janos K Lanyi, Sergei P Balashov, Viviana Gradinaru, Frances H Arnold,

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life. A member of this protein family, Archaerhodopsin-3 (Arch) of halobacterium Halorubrum sodomense, was recently shown to function as a fluorescent indicator of membrane potential when expressed in mammalian neurons. Arch fluorescence, however, is ... Read more >>

Proc. Natl. Acad. Sci. U.S.A. (Proceedings of the National Academy of Sciences of the United States of America)
[2014, 111(36):13034-13039]

Cited: 26 times

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Directed evolution of Gloeobacter violaceus rhodopsin spectral properties.

Martin K M Engqvist, R Scott McIsaac, Peter Dollinger, Nicholas C Flytzanis, Michael Abrams, Stanford Schor, Frances H Arnold,

Proton-pumping rhodopsins (PPRs) are photoactive retinal-binding proteins that transport ions across biological membranes in response to light. These proteins are interesting for light-harvesting applications in bioenergy production, in optogenetics applications in neuroscience, and as fluorescent sensors of membrane potential. Little is known, however, about how the protein sequence determines the ... Read more >>

J. Mol. Biol. (Journal of molecular biology)
[2015, 427(1):205-220]

Cited: 20 times

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Rapid synthesis and screening of chemically activated transcription factors with GFP-based reporters.

R Scott McIsaac, Benjamin L Oakes, David Botstein, Marcus B Noyes,

Synthetic biology aims to rationally design and build synthetic circuits with desired quantitative properties, as well as provide tools to interrogate the structure of native control circuits. In both cases, the ability to program gene expression in a rapid and tunable fashion, with no off-target effects, can be useful. We ... Read more >>

J Vis Exp (Journal of visualized experiments : JoVE)
[2013, (81):e51153]

Cited: 4 times

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Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.

R Scott McIsaac, Patrick A Gibney, Sunil S Chandran, Kirsten R Benjamin, David Botstein,

A conditional gene expression system that is fast-acting, is tunable and achieves single-gene specificity was recently developed for yeast. A gene placed directly downstream of a modified GAL1 promoter containing six Zif268 binding sequences (with single nucleotide spacing) was shown to be selectively inducible in the presence of β-estradiol, so ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2014, 42(6):e48]

Cited: 22 times

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Visualization and analysis of mRNA molecules using fluorescence in situ hybridization in Saccharomyces cerevisiae.

R Scott McIsaac, Sanford J Silverman, Lance Parsons, Ping Xu, Ryan Briehof, Megan N McClean, David Botstein,

The Fluorescence in situ Hybridization (FISH) method allows one to detect nucleic acids in the native cellular environment. Here we provide a protocol for using FISH to quantify the number of mRNAs in single yeast cells. Cells can be grown in any condition of interest and then fixed and made ... Read more >>

J Vis Exp (Journal of visualized experiments : JoVE)
[2013, (76):e50382]

Cited: 6 times

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Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.

R Scott McIsaac, Benjamin L Oakes, Xin Wang, Krysta A Dummit, David Botstein, Marcus B Noyes,

A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys(2)His(2) zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2013, 41(4):e57]

Cited: 50 times

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Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

R Scott McIsaac, Allegra A Petti, Harmen J Bussemaker, David Botstein,

In yeast, the pathways of sulfur assimilation are combinatorially controlled by five transcriptional regulators (three DNA-binding proteins [Met31p, Met32p, and Cbf1p], an activator [Met4p], and a cofactor [Met28p]) and a ubiquitin ligase subunit (Met30p). This regulatory system exerts combinatorial control not only over sulfur assimilation and methionine biosynthesis, but also ... Read more >>

Mol. Biol. Cell (Molecular biology of the cell)
[2012, 23(15):2993-3007]

Cited: 21 times

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Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.

Allegra A Petti, R Scott McIsaac, Olivia Ho-Shing, Harmen J Bussemaker, David Botstein,

Methionine abundance affects diverse cellular functions, including cell division, redox homeostasis, survival under starvation, and oxidative stress response. Regulation of the methionine biosynthetic pathway involves three DNA-binding proteins-Met31p, Met32p, and Cbf1p. We hypothesized that there exists a "division of labor" among these proteins that facilitates coordination of methionine biosynthesis with ... Read more >>

Mol. Biol. Cell (Molecular biology of the cell)
[2012, 23(15):3008-3024]

Cited: 18 times

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Coordinated regulation of sulfur and phospholipid metabolism reflects the importance of methylation in the growth of yeast.

Mark J Hickman, Allegra A Petti, Olivia Ho-Shing, Sanford J Silverman, R Scott McIsaac, Traci A Lee, David Botstein,

A yeast strain lacking Met4p, the primary transcriptional regulator of the sulfur assimilation pathway, cannot synthesize methionine. This apparently simple auxotroph did not grow well in rich media containing excess methionine, forming small colonies on yeast extract/peptone/dextrose plates. Faster-growing large colonies were abundant when overnight cultures were plated, suggesting that ... Read more >>

Mol. Biol. Cell (Molecular biology of the cell)
[2011, 22(21):4192-4204]

Cited: 24 times

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Does the potential for chaos constrain the embryonic cell-cycle oscillator?

R Scott McIsaac, Kerwyn Casey Huang, Anirvan Sengupta, Ned S Wingreen,

Although many of the core components of the embryonic cell-cycle network have been elucidated, the question of how embryos achieve robust, synchronous cellular divisions post-fertilization remains unexplored. What are the different schemes that could be implemented by the embryo to achieve synchronization? By extending a cell-cycle model previously developed for ... Read more >>

PLoS Comput. Biol. (PLoS computational biology)
[2011, 7(7):e1002109]

Cited: 5 times

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